Dear Amamda,
Not sure how much help I can be, but when my youngest daughter was 2 to almost 6, and her younger brother (3 yrs younger)was 2 1/2 to about 5 1/2 years old, I had the almost the same problem. My husband was in the military also, and was gone VERY frequently, a week or every other week, to a couple of months, to a year at a time in Vietnam. While they didn't "act out" as much as your son seems to be doing, they still had difficulty whenever my husband came home after a trip. They would have nothing to do with him, sit by him, on his lap, etc. for a while, they eventually would come around. How long usually depended on how long he had been gone. WE finally figured out that at the younger ages, they really just didn't remember him. So he just had to have patience and take things a little slowly until they got used to having him there again. AT about 4-4 1/2, they remembered
him, but then were scared he was going to "go away again", and were more reserved. They also had 2 older brothers and 1 older sister (I had 5 children in 9 yrs), so were used to not getting "all" the attention in the house. I think probably this is part of your son's problem. He has had you to himself for 9 months, and now he has to share you with what to him is a strange man. I am sure you are trying to do "family" things, but possibly if you could pick out some things that your son really likes to do, go to the park, the zoo, for a walk, bedtime reading, etc., and get him to do those just with him and his dad. Make them "only boy" things. As far as the potty goes, tell him everytime he goes to the potty like "a big boy again", he gets a "prize". Dollar Stores are great for this. Buy a few things at a time, put them in a "treasure box", and he gets to pick out 1 thing after the potty each time. Main thing for you and your husband is Patience! Good luck.